Protein target profile

VK055_4398

sulfite reductase (NADPH) hemoprotein, beta-component

Genome: KpATCC43816 Gene: cysI AIK82941.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GXH1
Length 570
Pocket druggability 0.921
Metabolic reactions 1
Chokepoint No
Direct ligand evidence 0 55 total records
Functional annotation 1 EC 13 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
No hit
Gut microbiome similarity
3.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
35.413 Higher values support similarity to known essential genes.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
95.43 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.921
Structure A0A0H3GXH1
Pocket Pocket 27
P2Rank 0.967
Structure A0A0H3GXH1
Pocket Pocket 1
ColabFold model
FPocket 0.903 · Pocket 27
P2Rank 0.948 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 151 / 4744 genomes with a hit
Prevalence 3.2%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Metabolic context: more central than 96.7% of genes in this genome, no human homolog detected.

Relative network centrality 96.7% more central than 96.7% of genes in this genome
Chokepoint Not a chokepoint
Catalyzed reaction

1 reaction mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MSEKHPGPLVVEGKLSDAERMKLESNYLRGTIAEDLNDGLTGGFKGDNFLLIRFHGMYQQDDRDIRAERAAQKLEPRHAMLLRCRLPGGVITTTQWKAIDKFAAENTIYGSIRLTNRQTFQFHGILKKNVKPVHQMLHSVGLDALATANDMNRNVLCTSNPYESQLHAEAYEWAKKISEHLLPRTRAYAEIWLDQKKVATTDEEPILGQTYLPRKFKTTVVIPPQNDIDLHANDMNFVAIAENGKLVGFNLLVGGGLSIEHGNKKTYARTASEFGYLPLEHTLAVAEAVVTTQRDWGNRTDRKNAKTKYTLERVGVETFKAEVERRAGIKFEPIRPYEFTGRGDRIGWVKGIDDKWHLTLFIENGRILDYPGRPLKTGLLEIAKVHQGEFRITANQNLIVASVPEDQKARIEKLARDHGLMNAVTPQRENSMACVSFPTCPLAMAEAERFLPSFIDKVEGVMSKHGVSDEHIVTRVTGCPNGCGRAMLAEVGLVGKAPGRYNLHIGGNRNGTRIPRMYRENITESEILDSLDELVGRWAKEREAGEGFGDFTVRAGIIRPVLDPARDFWE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 13 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

13
  • GO:0008652 The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • GO:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
  • GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0020037 Binding to a heme, a compound composed of iron complexed in a porphyrin (tetrapyrrole) ring.
  • GO:0004783 Catalysis of the reaction: hydrogen sulfide + 3 NADP+ + 3 H2O = sulfite + 3 NADPH + 3 H+.
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • GO:0009337 A multisubunit iron flavoprotein, which in yeast is composed of 2 alpha and 2 beta subunits. Catalyzes the reduction of sulfite to sulfide.
  • GO:0046872 Binding to a metal ion.
  • GO:0050311 Catalysis of the reaction: hydrogen sulfide + 3 oxidized ferredoxin + 3 H2O = sulfite + 3 reduced ferredoxin.
  • GO:0019344 The chemical reactions and pathways resulting in the formation of L-cysteine, 2-amino-3-mercaptopropanoic acid.
  • GO:0070814 The chemical reactions and pathways resulting in the formation of hydrogen sulfide, H2S.
  • GO:0000103 The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

32 records
Show feature table
Start End DB Term Name
425 567 Gene3D G3DSA:3.30.413.10 Sulfite Reductase Hemoprotein, domain 1
425 567 InterPro IPR045854 Nitrite and sulphite reductase 4Fe-4S domain-like superfamily
429 447 PRINTS PR00397 Sirohaem Fe-binding site signature
429 447 InterPro IPR006066 Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site
477 495 PRINTS PR00397 Sirohaem Fe-binding site signature
477 495 InterPro IPR006066 Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site
10 570 Hamap MF_01540 Sulfite reductase [NADPH] hemoprotein beta-component [cysI].
10 570 InterPro IPR011786 Sulphite reductase (NADPH) hemoprotein, beta subunit
148 340 FunFam G3DSA:3.30.413.10:FF:000004 Sulfite reductase [NADPH] hemoprotein beta-component
150 344 SUPERFAMILY SSF56014 Nitrite and sulphite reductase 4Fe-4S domain-like
150 344 InterPro IPR045854 Nitrite and sulphite reductase 4Fe-4S domain-like superfamily
13 142 SUPERFAMILY SSF55124 Nitrite/Sulfite reductase N-terminal domain-like
13 142 InterPro IPR036136 Nitrite/Sulfite reductase ferredoxin-like domain superfamily
346 422 SUPERFAMILY SSF55124 Nitrite/Sulfite reductase N-terminal domain-like
346 422 InterPro IPR036136 Nitrite/Sulfite reductase ferredoxin-like domain superfamily
428 559 SUPERFAMILY SSF56014 Nitrite and sulphite reductase 4Fe-4S domain-like
428 559 InterPro IPR045854 Nitrite and sulphite reductase 4Fe-4S domain-like superfamily
173 331 Pfam PF01077 Nitrite and sulphite reductase 4Fe-4S domain
173 331 InterPro IPR006067 Nitrite/sulphite reductase 4Fe-4S domain
425 567 FunFam G3DSA:3.30.413.10:FF:000003 Sulfite reductase [NADPH] hemoprotein beta-component
19 558 NCBIfam TIGR02041 assimilatory sulfite reductase (NADPH) hemoprotein subunit
19 558 InterPro IPR011786 Sulphite reductase (NADPH) hemoprotein, beta subunit
148 340 Gene3D G3DSA:3.30.413.10 Sulfite Reductase Hemoprotein, domain 1
148 340 InterPro IPR045854 Nitrite and sulphite reductase 4Fe-4S domain-like superfamily
12 565 PANTHER PTHR11493 SULFITE REDUCTASE [NADPH] SUBUNIT BETA-RELATED
12 565 InterPro IPR045169 Nitrite and sulphite reductase 4Fe-4S domain containing protein
353 416 Pfam PF03460 Nitrite/Sulfite reductase ferredoxin-like half domain
353 416 InterPro IPR005117 Nitrite/Sulfite reductase ferredoxin-like domain
81 138 Pfam PF03460 Nitrite/Sulfite reductase ferredoxin-like half domain
81 138 InterPro IPR005117 Nitrite/Sulfite reductase ferredoxin-like domain
477 493 ProSitePatterns PS00365 Nitrite and sulfite reductases iron-sulfur/siroheme-binding site.
477 493 InterPro IPR006066 Nitrite/sulphite reductase iron-sulphur/sirohaem-binding site

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #27
0.921
Likely same site as P2Rank 1 3.9 Å 28 shared residues 80% of smaller site
Unusual size
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.967
Likely same site as FPocket 27 3.9 Å 28 shared residues 80% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.251
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.148
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.048
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.018
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:434-434
UniProt: Binding site:440-440
UniProt: Binding site:479-479
UniProt: Binding site:483-483
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GXH1
AlphaFold DB full sequence Viewing
ColabFold VK055_4398
ColabFold full sequence Loaded

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

55 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 5 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
CMO PDB via homolog 28.0 Da · LogP -0.04 · TPSA 19.9 Open detail RCSB PDB
FES PDB via homolog Detail RCSB PDB
HOA PDB via homolog Detail RCSB PDB
NO2 PDB via homolog Detail RCSB PDB
SX PDB via homolog Detail RCSB PDB

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
CMO RCSB PDB P17846 28.0 Da LogP -0.04 TPSA 19.9 ✓ Ro5 ✓ Clean [C-]#[O+]
FES RCSB PDB O23813 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
HOA RCSB PDB Q76KB0 33.0 Da LogP -0.67 TPSA 46.2 ✓ Ro5 ✓ Clean NO
NO2 RCSB PDB P17846 46.0 Da LogP 0.25 TPSA 52.5 ✓ Ro5 ✓ Clean N(=O)[O-]
SX RCSB PDB P17846 48.1 Da LogP -0.34 TPSA 17.1 ✓ Ro5 ✓ Clean O=S

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.